ISTANBUL (Reuters) - The United States and Britain suspended non-lethal aid to northern Syria after Islamist fighters seized Western-backed rebel weapons warehouses, highlighting fears that supplies could end up in the wrong hands.

The rebel Free Syrian Army fighting President Bashar al-Assad said the U.S. and British moves were rushed and mistaken. "We hope our friends will rethink and wait for a few days when things will be clearer," FSA spokesman Louay Meqdad said.

In Washington, White House spokesman Josh Earnest said the United States was concerned about reports that Islamic Front forces had seized the buildings belonging to the Syrian Military Council, which is nominally in charge of the FSA.

"As a result of the situation ... the United States has suspended all further deliveries of non-lethal assistance into northern Syria," Earnest said, adding that humanitarian aid was not affected by the move.

The suspension underlines a crisis for the FSA leadership, which needs international backing to reinforce its credibility and to stop its fighters joining al Qaeda-backed Islamist militants who now dominate the war with Assad.

Fighters from the Islamic Front, which groups six major rebel brigades and which said last week it had quit the FSA, seized the headquarters of the Syrian Military Council and weapons warehouses at the Bab al-Hawa crossing on Syria's northwestern border with Turkey.

A U.S. official said FSA leader General Salim Idriss had fled into Turkey during the takeover of the warehouses, which contained trucks, food, medical packs and communication equipment including laptops and radios.

The Syrian Observatory for Human Rights, a British-based anti-Assad monitoring group, said the Islamic Front had seized anti-aircraft and anti-tank weapons from the SMC arms stores in fighting on Saturday.

The Islamic Front's battlefield success in capturing the stores could undermine SMC assurances to the United States that no supplies sent to their fighters would fall into the hands of Islamist brigades.

A U.S. embassy spokesman in Ankara said the situation was being investigated "to inventory the status of U.S. equipment and supplies provided to the SMC". Deliveries into southern Syria, through Jordan, would not be affected, he said.

Five rebel fighters were killed in the clashes at Bab al-Hawa, but it was not clear which side they were on.

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American aid, including trucks, ambulances and ready meals, reaches Syria overland through Turkey.

U.S. officials said in the summer that they had developed a system of distribution using SMC operatives that would ensure the aid reached U.S.-allied groups. The United States has been concerned the non-lethal aid should not reach Islamists.

A senior U.S. administration official said the suspension should not be misinterpreted.

"This is absolutely not the beginning of the U.S. washing its hands. We will remain engaged in the humanitarian effort. We will remain engaged in the diplomatic effort," the official said, adding: "This doesn't represent a change in policy in our support for the moderate opposition."

A Free Syrian Army fighter runs to avoid snipers loyal to Syria's President Bashar al-Assad in old Aleppo December 3, 2013.Mahmoud Hebbo

He said the administration was looking for other ways to see how the support can be provided to ensure it does not fall into the hands of "extremists".

The British wanted the situation clarified after the clashes. "We have no plans to deliver any equipment while the situation remains so unclear. We will keep this under close review," a spokesman from the British embassy in Ankara said.

Turkey shut its side of the border crossing in Hatay province, customs sources told Reuters, citing a reported increase in clashes on the Syrian side. There was no immediate confirmation from Turkish officials.

Wednesday's announcement does not affect humanitarian support because this is distributed through aid groups and the United Nations. The first U.N. relief airlift to Syria from neighboring Iraq will deliver food and winter supplies to the mostly Kurdish northeast over the next 10 days.

The 2-3/4 year conflict has killed more than 100,000 people, driven more than 2 million abroad as refugees and left many millions more dependent on aid.

Playing down the fighting between the Islamic Front and the FSA brigades as a "misunderstanding", the FSA's Meqdad said Idriss was talking to the front's leaders to try to resolve the confrontation.

Asked whether any FSA stock was missing Meqdad said: "Everything will be clear in the next hours, and we believe the Syrians are good people and we don't believe there was a problem. They are our brothers."

Infighting among Syrian rebels has weakened their efforts to bring down Assad in a conflict that began with peaceful protests against his rule in March 2011 and has descended into civil war.

"EXTREMISTS" THREATEN REBEL UNITY

"I ... want to underline that our support to the opposition remains undiminished," the British embassy spokesman said.

"We have been long-standing and strong supporters of General Idriss and the SMC. That remains the case. It is important that the SMC remains united in the face of attacks from the regime and from extremist groups.

"Otherwise this will be a setback for all Syrians who support a political solution and a democratic, pluralist future for their country."

Assad's army, backed by Lebanon's Hezbollah militant group and Iraqi Shi'ite fighters, has made steady gains around Damascus and to the north of the capital, while rebel territory in the north has seen increasing cases of inter-rebel conflict.

Many activists who helped to organize protests against Assad have now fled abroad from rebel-held territory, fearing not Assad's security forces but hard-line Islamists they say are equally intolerant of dissent.

Prominent human rights lawyer Razan Zaitouneh was kidnapped in the rebel town of Douma, activists said on Tuesday. They said it was not clear who had seized the 36-year-old activist, who has documented human rights violations in Syria.

The family of two Spanish journalists said on Tuesday they have been held since September by fighters linked to al Qaeda.

Fifty-five journalists have been killed and 30 are still missing in Syria, according to the New York-based Committee to Protect Journalists, making the country the most dangerous place in the world for media workers.

Writing by Dominic Evans, additional reporting by Lesley Wroughton and Roberta Rampton in Washington, and Yara Bayoumy in Dubai, editing by Peter Millership, Will Waterman and David Stamp